News Archive
"From the genome to the tree of life"

ARCHIVES - Deep Gene in the News

National Geographic June 4th, 2001
A news brief about the evolution of all multicellular land plants from only one lineage of algae, even though three other algal lineages made the transition from water to land. Commentary by UC Berkeley's Brent Mishler and Louisiana State's Russell Chapman.
The Advocate ONLINE  May 29, 2001
Article on Cephaleuros, Magnolias, and Deep Green/Deep Gene by Marlene Naanes
The Scientist 15[5]:12,  March 5, 2001 *** you need to be registered with the Scientist to view this article ***
'Deep Gene' and 'Deep Time' Evolving collaborations parse the plant family tree  by Barry A. Palevitz
Financial Times  March 3, 2001
The Nature of Things: A project to unravel the ancestry of today's flora has produced a surprise  by Clive Cookson
Science Online Febuary 19, 2001*** you need to be registered with Science Online to view this article ***
Invasions of the Algae; green algae and Deep Gene, by Jay Withgott
UC Berkeley Press Release  Febuary 16, 2001
Deep Green spawns Deep Gene and Deep Time... by Robert Sanders
NSF News January 31, 2001
Scientists Shake Up "Family Tree" of Green Plants

National Geographic June 4th, 2001 [top]
All Land Plants Evolved From Single Type of Algae, Scientists Say
Charleston Daily Mail
June 4, 2001

The first tentative moves that got life out of the water and onto the land eons ago were apparently made by slimy green algae, scientists say, and coming ashore wasn't easy.
According to paleobotanist Russell Chapman of Louisiana State University, the first algae that managed to gain residence on terra firma-finally kick-starting the evolution of land plants-must have come out of fresh water, not the sea.

And, Chapman said, even though four distinct types of algae managed to come ashore, only one of them evolved enough complexity to eventually cover the land with vegetation, what we now call trees, shrubs, flowers, and grass. Nonetheless, all four species of pioneering algae can still be found on land, he said.

The ancient history of land plants is becoming evident because of recent advances in techniques for genetic analysis. It's now possible to look at individual genes in algal cells and higher plants and calculate their similarity. Clues to the history of such organisms lie within the chemical "spelling"-the sequence similarity-of the organisms' genes. The closer they resemble each other, the closer they are related.

"The evolutionary history of various genes can be studied within the lineage of green algae," Chapman said, and that is what offers vital clues to how the algal genes eventually evolved to produce plants. Today's green plants are enormously varied, from the giant redwood trees to the tiniest weeds-everything that blooms, including our crops.

All Plants Rose From Single Type of Algae

Chapman was speaking earlier this year during a symposium on the genetics and evolution of green plants at the annual meeting of the American Association for the Advancement of Science in San Francisco. He and several colleagues made it clear that today's multicellular plants, such as corn, cabbages and all the other greenery, arose from a single type of algae.

As noted by plant geneticist Brent Mishler of the University of California at Berkeley, the genetic evidence now being uncovered shows that "the multicellular land plants are all of one lineage. The fossil evidence suggests that others (types of algae) tried," but they failed to evolve the needed complexity. In other words, the three other algae that managed to wade ashore didn't evolve beyond the single-cell stage, so they remain what they were, algae.

The discoveries and the ideas of how land plants arose "reminds people of our humble origins," Chapman added. "This reminds people of how important algae are in general, since without that one escape from water and subsequent evolution, the half million species of plants that are so important to life on Earth might not exist. There would be no crops, no flowers, no fibers or foods. Also no us, of course."

(C) 2001 Charleston Daily Mail

The Advocate ONLINE  May 29, 2001 [top]

In the summer, the creamy-white flowers of thousands of magnolia trees in yards and wilderness areas across the state emit a rich fragrance.

The magnolia became the state flower in 1900 because of its abundance in Louisiana. Scientists then did not know the flower had more to offer than beauty and fragrance. Its leaves also offer a clue to the past that would later let scientists look back into the history of land plants about 500 million years ago.

The key to the past is an alga that lives on the leaves of the magnolia tree. Cephaleuros virescens is a species of green alga which contains an orange pigment that grows on the leaves, resembling an orange, velvety disc.

The significance of that alga is that it came from algae that originated in marine, or salty, water about 500 million to 600 million years ago, which made it a contender for the title of first form of green life on earth.

However, freshwater algae endured foreign environmental conditions hundreds of millions of years ago, which shifted their preferred environment from water to land.

Those freshwater algae not only became the only form of green life on land at that time, they also gave rise to every form of green life on the Earth today, including Louisiana's magnolia trees.

A professor and researcher at LSU, Russell Chapman, studied the origins of green plants with about 200 researchers around the world in a project called Deep Green.

The project answered questions about the evolution of green plants, including the possible species that gave rise to all land plants.

"Understanding the evolution of green plants is important because plants are so important," said Chapman, executive director of the Center for Coastal, Energy and Environmental Resources. "We use plants for food, medicines and shelter."

The project, which just wrapped up this year, revealed that all land plants come from a single line of freshwater green algae called Charophyceae. Scientists determined these algae were the origin of all plants after the scientists performed rounds of tests on the alga's DNA, cell division processes and morphology.

Before the Deep Green project, scientists did not know the algal key players in the evolution of all land plants.

Chapman's research assistant, Debra Waters, equates the discovery of Charophyceae to finding the missing link in human evolution from apes.

The discovery was also interesting because it had seemed more likely that the origin of all plants was a marine alga. Some marine algae have the ability to alter life processes to survive harsh environments. Every time a tide rises or falls, their living conditions change drastically.

Since the move from water to land would create harsh conditions for a water alga, a marine alga that could alter its life processes was more fit for a move than a freshwater alga.

Yet, the freshwater algae prevailed as the original land dwelling plant, much to the fascination of Chapman and Waters.

Deep Green also provided critical genetic information by outlining a genealogy of plants and algae.

The plant family tree not only revealed the evolution of green plants, but detailed some aspects of plant and algal genetic layout. It also detailed the organisms' biological processes, which will allow scientists to compare species.

A project that generates that much information is significant for several reasons, including getting questions answered before any more plants become extinct, Chapman said.

"If a certain plant is known to produce a helpful compound, it's helpful to know of a related plant," Chapman said. "Because if the (original) plant doesn't grow well, you can see if relatives have a similar compound."

Deep Green research also can be applied to genetic engineering of crop plants, he said.

"Knowing how certain structures and processes evolved could help us learn how to improve them," he said.

Scientists may be able to control when a crop plant will produce leaves or flowers using the genetic information from Deep Green, said Linda Graham, a professor of botany and environmental studies at the University of Wisconsin-Madison who was also involved in Deep Green.

Controlling growth of a plant will also control when it produces its edible portion, Graham said.

Scientists, now knowing which genes evolved to produce certain proteins in plants, can use that information to engineer a plant to produce more of that protein, Chapman said.

Though Deep Green answered some questions about the evolution of plants, scientists still have many more.

Two projects that will continue to develop research from Deep Green are in the works.

Deep Time will detail the emergence of flowering plants and the relationship between existing plant families by studying plants' fossil record and living plants.

Deep Gene will choose plants for complete DNA sequencing.

"It's important to understand these things to understand life," Waters said. "It's most exciting to know how things are intertwined."


Advocate staff photo by Bill Feig
Among 200 scientists studying the evolution of green plants, Russell Chapman, left, looks over magnolia leaves with Debra Waters and Juan Lopez-Bautista.

The Scientist 15[5]:12,  March 5, 2001 [top]

'Deep Gene' and 'Deep Time'

Evolving collaborations parse the plant family tree
By Barry A. Palevitz

Amid last month's hoopla over the human genome sequence and what it says about humans, plant biologists announced two new efforts aimed at a firmer understanding of plant evolution--who is related to whom and how--a discipline better known as systematics. Constructing evolutionary family trees is harder than investigating personal genealogies--biologists don't have the equivalent of birth registrations or family bibles to consult. Fossils tell them what ancient plants use to look like, but placing them in context with living organisms is difficult at best. Even the systematics of existing plants can be contentious, as researchers disagree on lumping plants together or splitting them apart in search of the most natural taxonomy.

Scientists liken constructing phylogenetic trees to tracing all the branches and trunks of a real tree, like an oak, with only characteristics of its outermost twigs to go on. That's because present day organisms are the sole survivors--called "terminals" by systematists--of multiple, diverging lineages. However daunting the process, researchers have made breathtaking progress in the last 20 years, thanks to gene sequencing. According to University of Georgia systematist David Giannasi, "it was a case of technology catching up with theory." By comparing DNA sequences such as those encoding ribosomal RNA and chloroplast proteins, systematists redrew large chunks of the plant taxonomic map.

A good example of the redefining process is found in the milkweeds, which taxonomists traditionally placed in a family called the Asclepiadaceae. They also thought the milkweeds were allied with a second family, the Apocynaceae. But based on molecular data, "the Asclepiadaceae nests within the Apocynaceae," says Giannasi, "so we now know they should be lumped together." The same is true for the mints, thought to be in their own family just a few years ago but now grouped with the verbenas.

Researchers have also clarified some of the most basal groups in the plant family tree. They now know that a previously obscure New Caledonian shrub called Amborella is sister to all other flowering plants, or Angiosperms, with water lilies branching off the evolutionary trunk at the same level or just above.1 They also think the gnetales, previously considered flowering plant allies, are probably more closely related to pines, in the Gymnosperms.2 And horsetails and whisk ferns, once thought to relic descendents of early land plants, now seem more closely tied to the true ferns.3

Feds Fertilize Interactions

One of the key ingredients in systematists' recipe for success was cooperation and communication. Thanks to joint funding starting in 1994 from the U.S. Department of Agriculture, Department of Energy, and National Science Foundation, a consortium of researchers called the Green Plant Phylogeny Research Coordination Group, or Deep Green, pooled ideas and resources in a joint plan of attack. Machi Dilworth, head of NSF's Division of Biological Infrastructure, thinks, "Deep Green was one of the very visible success stories" of the three agency effort. "With a little support they were able to come together and accomplish major scientific achievements."

NSF was so impressed with the collaborative approach, it decided to fund "Research Coordination Networks" (RCNs) serving all areas of the biological sciences. Like Deep Green, the grants foster communication and collaboration between scientists, but don't directly cover research costs funded by other programs. Two of the RCNs are scions of Deep Green.

Systematists Dip Into Genomics

In one of the team projects, called Deep Gene, systematists join forces with molecular biologists working on entire genomes like those of Arabidopsis and rice.4,5 By tracing suites of genes that govern processes such as flower development, they hope to clarify mechanisms governing major evolutionary changes, including new biochemical pathways and the appearance of complex morphological characters. Sequencing also uncovers large-scale genomic changes including chromosomal rearrangements, which can be invaluable in defining plant relationships. Likewise, evolution depends on alteration in spatial and temporal controls governing gene activity--when and where genes turn on and off. The new RCN hopes to discover how gene regulation changed in the evolution of various plant groups.

Tolerance toward desiccation is a good example of how traits may have appeared and disappeared during evolution. The first plants to occupy dry land faced a big problem compared to their aquatic ancestors: an uncertain supply of water. Mosses, for example, grow in moist environments but also suffer periodic drying. That's why they require biochemical mechanisms that allow them to survive dry periods. When larger vascular plants arose, with roots and a plumbing system to extract water from the soil and move it long distances, desiccation tolerance became less important. But it reappeared later on in seed plants, which remove water from tissues surrounding young embryos in preparation for dormancy.

According to Deep Gene principal investigator Brent Mishler of the University of California at Berkeley--and a veteran of Deep Green--"around 80 genes are involved in desiccation tolerance in mosses. When desiccation re-evolved in seeds, some of these genes were reused." Mishler would like to know how such changes in gene regulation arose during major evolutionary events. Mishler chaired a symposium on Deep Green at the annual meeting of the American Association for the Advancement of Science, February 15-20, in San Francisco.

Daphne Preuss, molecular biologist at the University of Chicago and Deep Gene co-PI, says she brings to the table "the tools and techniques of high throughput, big scale biology." Still, in a true collaboration everybody benefits. With Deep Gene, genomicists like Preuss want to advance their own projects. In her case, that means figuring out how centromeres work. Centromeres are DNA sequences located where chromosomes attach to spindle fibers during mitosis and meiosis. Preuss has dissected centromeric DNA in Arabidopsis but knows that "the sequences are very diverse from organism to organism." The question is, "how did these differences evolve, and what key components are important for centromere function?" Adds Preuss," I want insight from looking at conservation through evolution."

Preuss admits that "this is expensive work, so every decision counts. We're now making key decisions as to which species to look at next. We're looking to people in phylogenetics to help." Mishler sees other practical benefits from Deep Gene. "Can we use the information for agriculturally important plants that aren't desiccation tolerant?" he asks. By guiding researchers to promising sources, Deep Gene can also "predict useful chemicals for pharmacology," says Mishler. That makes University of Georgia's Giannasi smile because older studies comparing the chemical composition of plants--including substances such as terpenoids--predicted changes cemented by more recent gene sequencing projects. "The secondary chemistry was there, but nobody trusted it," comments Giannasi.

Fossils and Morphology Join the Fray
Doug and Pamela Soltis of Washington State University in Pullman lead another RCN called "Deep Time." Having done much of the gene sequencing for Deep Green, the Soltis' want to superimpose other kinds of information on their phylogenetic trees, and in the process add the dimension of time to key points in plant evolution.

Years before systematists accessed gene sequences, they relied on other information in the form of morphological, anatomical and chemical characters. While valuable, such characters can be misleading. For example, a structural trait shared by two groups could have arisen by convergent evolution rather than common ancestry (though the same applies to DNA sequences). Moreover, the number of structural characters applicable to phylogenetic analysis is limited; DNA sequences, on the other hand, are far more useful since the average protein encoding sequence contains 1,000-2,000 characters, or nucleotides. That's why they turned to genes.

But the tide may be changing again, at least a little. The Deep Time RCN will arrange plants according to a "morphological matrix" of characters, but "constrain the taxa to conform to the DNA-based topology already available, and in which we have good confidence at this point," say Pam and Doug Soltis. They'll then "conduct a phylogenetic analysis of the morphological matrix with fossils included." The trick will be to pick characters from existing plants that also apply to fossils. Despite the fact that "fossils have rarely been integrated in a phylogenetic context for any group," the Soltis' are hopeful. Since dates are available for many of the fossils, their inclusion adds a time factor to the phylogenetic tree--systematists can assign dates to key branch points. They'll also integrate data from molecular clocks governed by mutations. "It's sort of like the movie Back to the Future,'' note the Soltis', "Having the timing of a key event in the past nailed down is critical in understanding what has occurred to produce what we see in the present."

The Soltis' also wax philosophical about the collaboration: "We spent a decade in the area of systematics largely focused on molecules. There is a wealth of information in nonDNA characters such as morphology and anatomy, and we can't lose expertise in these areas."

Problems? Cooperation is the Key

Deep Gene and Deep Time researchers realize that reaching their goals may not be easy. According to the Soltis', "two big issues are missing data and the combinability of molecular and morphological data sets." Mishler agrees: "We don't know entirely how to do it. Theory hasn't kept pace--it's dealt mostly with sequence data." Researchers hope the latest collaborations will foster development of new methods to tackle such problems. Mishler sees promise. "The RCN will help us. Even a small amount of data from these other sources can improve phylogenetic trees" and eventually "lead to more research funding." The depth of cooperation is all the more impressive because deep Gene and Deep Time will interact.

The "Deep" projects testify to the importance of collaboration in modern research. According to Doug Soltis, "the cooperative nature of botanists has really turned the tide in the past decade." Mishler agrees that "research would have gone on, but it would not have made the progress it did." Preuss taps federal agencies for greasing the skids. "Some of these things are initiated by granting incentives, so I think it's wise. It's good to stir the pot and mix people together." Adds Machi Dilworth of NSF, "we would like to foster communication among scientists, to advance science through collaboration and coordination."

Barry A. Palevitz ( is a contributing editor to The Scientist.

1. B.A. Palevitz, "Discovering relatives in the flowering plant family tree," The Scientist, 13[24]:12, Dec. 6, 1999.
2. L.M. Bowe et al., "Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers," Proceedings of the National Academy of Sciences, 97:4092-97, April 11, 2000.
3. K.M. Pryer et al., "Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants," Nature, 409:618-22, Feb. 2, 2001.
4. B.A. Palevitz, "Arabidopsis genome. Completed project opens new doors for plant biologists," The Scientist, 15[1]:1, Jan. 8, 2001.
5. B.A. Palevitz, "Rice genome gets a boost," The Scientist, 14[9]:1, May 1, 2000.

Financial Times  March 3, 2001 [top]
BODY AND MIND: Plants that made the leap from the deep: THE NATURE OF THINGS: A project to unravel the ancestry of today's flora has produced a surprise, writes Clive Cookson
Financial Times; Mar 3, 2001

Botanists have drawn up the first authoritative "tree of life" for the plant kingdom. One surprise is the finding that all land plants are descended from a green alga that emerged from a lake or river less than 500m years ago.Many scientists had thought that plants came out of the sea, rather than fresh water, and that plants successfully invaded the land on more than one occasion.

The project, known as Deep Green and funded mainly by the US government, has involved 200 botanists using the latest genetic techniques to unravel the relationship between today's plants and their ancestors. Their latest discoveries were described last week at the American Association for the Advancement of Science meeting in San Francisco.

The ancestor of all today's land plants, from mosses to ferns, roses to redwood trees, turns out to be a single-celled green alga that emerged from fresh water about 470m years ago. That was 70m years after the great proliferation of invertebrate animals, including many multicellular creatures, that had taken place in the oceans during the so-called "Cambrian explosion".

The plants' emergence from the water enabled animals to follow - first arthropods (the ancestors of insects and spiders) and then our own vertebrate ancestors. "Animals could not move on to land until there were some plants there for them to eat," says Deep Green project leader Brent Mishler of the University of California, Berkeley.

Once on land, the plants diversified fast. The ancestors of today's ferns and horsetails split off from the main lineage of land plants about 400m years ago. At that time all plants were small, growing a few centimetres high at most, and they reproduced by spores. The first trees appeared in the Carboniferous period 300m years ago. And soon afterwards seeds and pollen evolved, as a more efficient means of reproduction than simple spores.

But flowers - a further reproductive refinement - did not appear until about 120m years ago, during the age of dinosaurs. Even after Deep Green, "the origin of flowers is one of the great continuing mysteries of plant biology," says Claude de Pamphilis of Pennsylvania State University.

Flowering plants have the advantage of protecting their seeds in the fleshy bodies of their fruits - in contrast to more primitive plants such as conifers that carry "naked seeds". The closest living relation to the first flowering plants appears to be an obscure cream-coloured flower called amborella that is found today only on the South Pacific island of New Caledonia.

The last really important evolutionary step for plants - and the animals that depend on them - was the appearance of grasses in the middle of the Tertiary period, about 30m years ago. Grasslands, which today form important ecological habitats such as savannas, steppes and prairies, are therefore a relatively recently development.

Within the overall Deep Green story some fascinating strands of inquiry emerge. Take that first step from water to land. Although a single lineage of green algae, the charophyceae, gave rise to all land plants, it turns out that the other three main groups of green algae conquered the land, too - but they just did not get anywhere.

Russ Chapman, a Deep Green biologist at Louisiana State University, in Baton Rouge, is particularly interested in the obscure algal group called trentepohliales, which specialise today in growing above ground on trees, walls and rooftops. Although these algae grow mainly in the tropics, they are also common in the damp and mild conditions of western Ireland, where several species form orange and red mats on stone and tree bark. (The orange colour of the carotenoid pigments in the trentepohliales overwhelms the green of the chlorophyll that is also present.)

Chapman hopes that further research will give some clues about the reasons why the trentepohliales - which emerged from the sea rather than fresh water - seem to have hit an evolutionary dead-end.

One of the most important adaptations made by algae to life on land was to tolerate desiccation. "When plants first invaded the land, they were all vegetatively tolerant - they could dry up completely and still be rejuvenated," Mishler says. "But as plants evolved more complicated structures, they lost this ability.

"The interesting story is that desiccation tolerance re-evolved at least eight times within flowering plants, and again when the seed evolved. It appears from our initial work that many of the genes involved in seed desiccation tolerance are descendants of the early genes that were involved in vegetative desiccation tolerance in the first place."

The researchers hope that, if they can understand the group of genes that enable primitive plants to withstand desiccation, they will find a way to breed crops that live on less water or survive drought better.

Now that Deep Green is drawing to a close, the US National Science Foundation has agreed to fund two successor projects. The first, called Deep Time, will explore in greater detail the emergence of flowering plants and the relationship between existing plant families, by studying both the fossil record and living plants. The second project, Deep Gene, will choose the most representative selection of plants for complete DNA sequencing.

At the same time, the foundation is considering a grander project, modelled on Deep Green, which would generate a definitive tree of life for all creatures, including not only plants but also bacteria and animals.

Copyright: The Financial Times Limited 1995-1998

Science Online Febuary 19, 2001 [top]

Invasions of the Algae

SAN FRANCISCO--A revised family tree of plants brings surprising news about how ancient algae moved onto land to give rise to terrestrial plants--everything from pines to palms to petunias. The conquest of land happened four different times, researchers said here on 17 February at the annual meeting of the American Association for the Advancement of Science, ScienceNOW's publisher. But only one group of invaders successfully diversified into today's land plants, and it came from a source researchers once considered unlikely: freshwater lakes or ponds.

Traditionally, biologists thought terrestrial plant life must have arisen from the oceans. Marine algae, adapted to the salty sea environment, seemed much better at retaining water than their freshwater counterparts, and thus at living on land, where dehydration is a constant threat. Tidepool algae seemed the most likely candidate predecessors of land plants, but recently, botanists comparing the anatomy of plants began to suspect that freshwater algae were the real ancestors.

Researchers collaborating in the international "Deep Green" project are addressing such questions by putting together a massive phylogeny, or family tree, of the green plants, based on a comparison of their genes and phenotypes. Armed with this history book, they now can trace the evolution of traits through time and across species. Their tree indicates that all modern land plants are descendants of a single group of freshwater algae called charophytes. But the tree also reveals three other, less successful conquests, Russell Chapman of Louisiana State University told the meeting. Only one of these originated in saltwater; it gave rise to the Trentepohliales, a group of 60 species of rock- and tree-hugging algae that look like orange fuzz.

Why freshwater algae diversified into the 300,000 or so land plant species that blanket the Earth, while the marine ones never took off, is unclear. But Chapman suggests that marine invaders, adapted to saltwater, may face a steep challenge from the freshwater they'd experience on land in the form of rain. Interestingly, the algal lineages that moved onto land all share a type of cell division, called phragomoplastic, that other algae lack, but Chapman says it's not yet clear how or whether this trait might have aided a shift onto land.

Rick McCourt, curator of botany at the Academy of Natural Sciences in Philadelphia, praises the work, but says additional plants added to the analysis in the future could increase the number of known invasions of land. Deep Green researchers are now engaged in "Deep Gene," an attempt to integrate the phylogenetic data with information from whole genome sequences of plants. This may allow them to trace the evolution of gene complexes involved in traits such as desiccation tolerance and cell division, says Brent Mishler of the University of California, Berkeley--and perhaps to determine whether groups like the charophytes have special features that spur diversification.


It came from the sea. Trentepohlia, which grows on bark, is one of the few terrestrial algae that evolved from saltwater ancestors--but it was freshwater algae that gave rise to the land plants.

UC Berkeley Press Release  Febuary 16, 2001 [top]

Deep Green spawns Deep Gene and Deep Time to continue work toward a complete tree of life for the green plants
16 February 2001
By Robert Sanders, Media Relations

San Francisco - The highly successful Deep Green project to construct a "tree of life" for the green plants has ended, but it has seeded new projects to strengthen the branches and root the tree more firmly in new genetic and fossil data.
Among these projects is "Deep Gene," headed by University of California, Berkeley, botanist Brent D. Mishler, and "Deep Time," headed by Doug Soltis of the University of Florida. The National Science Foundation (NSF) has agreed to fund both projects with $500,000 each over the next five years.

The success of Deep Green also has emboldened NSF to float the idea of a much larger project - generating the definitive tree of life for everything, from bacteria to bats, fungi to flowering plants. NSF director Rita Colwell calls Deep Green one of the best investments the foundation has made, Mishler said.

Mishler and four colleagues will brief reporters Feb. 16 at 11 a.m. about the accomplishments of Deep Green and its proposed offshoots. Mishler, a spokesman for Deep Green, is director of UC Berkeley's University and Jepson Herbaria and a professor of integrative biology in the College of Letters & Science.

Deep Green has contributed to more than 100 research papers, Mishler said, the latest of which, in the Feb. 1 issue of Nature, nailed down the sister group of the seed plants. The work, coauthored by Kathleen Pryer and Harald Schneider of Chicago's Field Museum of Natural History and Alan R. Smith and Ray Cranfill of the UC Berkeley Herbarium, provided very strong evidence that ferns and horsetails are one another's closest relatives and the group most closely related to the seed plants.

"It clarifies one big chunk of the tree," Mishler said. "We haven't completed the whole tree, but these papers one at a time have dealt with all aspects of the green part of the tree of life."

The Green Plant Phylogeny Research Coordination Group, initially funded for a five-year period by the U.S. Department of Energy, NSF and the Department of Agriculture, was initiated by plant biologists as a way to make sense of the reams of data on plant relationships.

In a series of meetings over the past five years, more than 200 biologists reached consensus on the most important plants to target in genetic studies and the best genes to focus on. Workshops and a Web site clearinghouse for phylogenetic information helped the community of plant biologists coordinate research and answer important questions about plant relationships.

"It is important to emphasize that this field used to be very independent and lab-oriented, where everyone was working in secrecy within the walls of their lab," he said. "But as a result of Deep Green, people began to cooperate. They started sharing data and techniques, and that's where this progress came from."

Among Deep Green's achievements was completion of a good draft of the tree of life for green plants. It identified a cream-colored flower called Amborella as the earliest-diverging lineage in the flowering plants; concluded that land plants first emerged onto land from fresh water, not the salty oceans; and made clear that, at many critical transitions in evolution, only one lineage of green plant survived.

Such information on plant relationships becomes extremely important as researchers try to engineer new traits -from disease resistance to drought tolerance - in crop plants.

With Deep Gene, funded through a Research Coordination Networks grant from NSF, Mishler hopes to repeat the success of Deep Green. This time, however, he is bringing in scientists working on plant genomics to reach consensus on the most important plants to target for genome sequencing.

The genome sequence of the widely-used research plant Arabidopsis thaliana is nearly complete, and sequencing of the rice and corn genomes is underway. Genomic data is publicly available on some 19 other plants. To make the most of sequencing efforts, Mishler said, scientists should choose more diverse plants that cover the range of economically important land plants.

"You have to pick the landmarks. If you want a good representation of the whole tree of life, you need to pick genomes nicely spaced on the tree," he said. "Then, for example, once you understand the genes involved in flower development in one species, it's not too difficult to probe for the genes involved in flower development in nearby species."

He notes that the long-term goal of plant genomics is to identify, isolate and determine the function of genes associated with various plant traits. This can be facilitated by a quality tree of life. Using sister group comparisons, for example, researchers can locate two closely related plants, one with a particular trait and one without, to help them reduce the number of genes they need to look at to isolate those responsible for the trait.

"Ideally, you could narrow the search down to probably just a few genes from thousands," he said.

Alternatively, ancestor-descendent comparisons allow researchers to study complex systems of interacting genes, such as those controlling the angiosperm flower, at a more primitive evolutionary stage, for example, when they were involved in moss and fern reproduction.

One area where this approach has borne fruit is the study of dessication tolerance, the ability of plants to withstand drought. If the trait, common in algae, ferns and lichens, can be transferred to crop plants, they might subsist on less water or better survive drought.

In a report in last November's Journal of Plant Ecology, Mishler and U.S. Department of Agriculture researcher Melvin J. Oliver used sister group comparisons to help unravel this complex phenotype, which involves more than 80 interacting genes.

"When plants first invaded the land, they were all vegetatively dessication tolerant - they could dry up completely and still be rejuvenated. But as plants evolved more complicated structures, they lost this ability," Mishler said.

"The interesting story is, dessication tolerance re-evolved at least eight times within flowering plants, and again when the seed evolved. It appears, from our initial work, that many of the genes involved in seed dessication tolerance are descendents of the early genes that were involved in vegetative dessication tolerance in the first place."

These findings emphasize the value of studying simpler plants to better understand higher plants, Mishler said.

"We now have real hope that we will be able to understand something about these economically very important events in evolution, the evolution of the seed and of the flower, by looking at mosses and ferns and algae, which are much simpler study systems," he said.

More insights are sure to come from the interaction between systematists like Mishler, who chart the evolutionary relationships among plants, and genomicists identifying the genetic makeup of green plants.

"Deep Gene is an attempt to meld together the plant phylogenetics progress we've made rapidly in the last few years with the rapid progress in plant genomics," Mishler said. "We believe this will be a truly synergistic process, where genomicists and phylogeneticists both benefit."


NSF News January 31, 2001 [top]
Scientists Shake Up "Family Tree" of Green Plants
Apparently, the lowly fern deserves more respect.

New research scheduled to appear as the journal Nature’s cover story on February 1 concludes that ferns and horsetails are not -- as currently believed -- lower, transitional evolutionary grades between mosses and flowering plants. In fact, ferns and horsetails, together, are the closest living relatives to seed plants.

"Today's systematists are using genomic tools to re-write the textbooks on animal and plant evolution," says James Rodman, program director in NSF's division of environmental biology, which funded the research. "This research is the latest major rearrangement of the plant tree of life. It will encourage others to explore ferns as model organisms for basic ecological and physiological studies."

The research calls for rethinking the "family tree" of green plants, according to scientists. Also, it uncovers a research shortcoming: All main plant model organisms used for research (such as Arabidopsis, which became the first plant to have all its genes sequenced) are recently evolved flowering plants.

This limitation could compromise scientific research. Models in the newly identified fern and horsetail lineage are needed to round out the study of plant development and evolution. This could help scientists fight invasive species, engineer genetic traits, develop better crops and prospect the botanical world for medicines.

The new research uses morphological and DNA sequence data to show that horsetails and ferns make up one genetically related group, which evolved in parallel to the other major genetically related group made up of seed plants and including flowering plants.

"Our discovery that 99 percent of vascular plants fall into two major lineages with separate evolutionary histories dating back 400 million years. It will likely have a significant impact on several disciplines, including ecology, evolutionary biology and plant developmental genetics," said Kathleen Pryer, lead author of the paper and assistant curator in botany at The Field Museum in Chicago. "Viewing these two genetically related groups as contemporaneous and ancient lineages will likely also have profound consequences on our understanding of how terrestrial ecosystems and landscapes evolved."

The work of Pryer and her colleagues builds on the Deep Green project, a collaboration of researchers dedicated to uncovering the evolution of and interrelation of all green plants. In 1999, Deep Green reported at an international botanical conference that DNA analysis indicates that all green plants -- from the tiniest single-celled algae to the grandest redwoods -- descended from a common single-celled ancestor a billion years ago. Green plants, which include some 500,000 species, are among the best-documented groups in the tree of life.


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